I like the idea of Necron being the last boss. A big theme of FFIX is that no matter what all the human/humanish villians turn good in the end showing even the most evil guys can become good. But Necron was death itself (hence the Necro part of his name) He was pure death meant to only to end all life, by destroying the crystal when he had received the signal life was ready to end. Which came when Kuja wanted to end life.

Also he is foreshadowed before hand a few times. But he's never out right mentioned.

I thought he was really a good final boss.